SAXSdb — 3oah

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein VP1

Adeno-associated virus - 6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	6-AMINOPYRIMIDIN-2(1H)-ONE × 60 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine × 60 water × 60	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	6-AMINOPYRIMIDIN-2(1H)-ONE × 1 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	6-AMINOPYRIMIDIN-2(1H)-ONE × 5 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine × 5 water × 5	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	6-AMINOPYRIMIDIN-2(1H)-ONE × 6 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine × 6 water × 6	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	6-AMINOPYRIMIDIN-2(1H)-ONE × 1 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine × 1 water × 1	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 10	6-AMINOPYRIMIDIN-2(1H)-ONE × 10 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine × 10 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O56137_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–534； UniProt 203–736

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3oah
Deposition date deposition_date	2010-08-05
Structure title title	Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6
Keywords keywords	Beta-barrel, ssDNA binding, ssDNA, icosahedral virus, virus; VIRUS
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3oah__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3oah__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3oah__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	0.00 Å
Rg (electron density)	108.80 Å
Total Rg	109.10 Å
Atom count	248820
Residues	31140
Excluded volume	4357200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3oah__assembly_1__model_1`	60-MERIC （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3oah__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3oah__assembly_3__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3oah__assembly_4__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3oah__assembly_5__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`3oah__assembly_6__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	59664.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4158

MASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL

Source Source

Source organism organism	Adeno-associated virus - 6
NCBI taxonomy ID ncbi_taxonomy_id	68558
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	6-AMINOPYRIMIDIN-2(1H)-ONE
Molecular weight formula_weight	111.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine
Molecular weight formula_weight	331.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3oaha_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

CATH v4.4 (1 domains)

Domain ID domain_id	3oahA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

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Unit-cell length a length_a	263.000 Å
Unit-cell length b length_b	263.000 Å
Unit-cell length c length_c	609.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	180

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2747
R_free r_free	0.2875

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein VP1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3oah__assembly_1__model_1

3oah__assembly_1__model_1 | I(q)

3oah__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein VP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3oah__assembly_1__model_1

3oah__assembly_1__model_1 | I(q)

3oah__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)